Population genetic history of the ancient reindeer-herding Ewenki people

Abstract

Aim: High-quality genomic resources from underrepresented populations are essential for understanding human genetic origins, population structure, and demographic history. The Ewenki, an ethnolinguistic minority mainly inhabiting the high-latitude, cold regions of Northeast China, remain insufficiently characterized at the genome-wide level. This study aimed to investigate the population structure, ancestral composition, and demographic history of the Ewenki to provide insights into human genetic evolution in Northeast Asia.

Methods: We generated genome-wide single-nucleotide polymorphism (SNP) data from 46 Ewenki individuals in Inner Mongolia and merged them with public modern and ancient genomic datasets. Population structure and demographic history were reconstructed through Principal component analysis (PCA), model-based ADMIXTURE, fineSTRUCTURE haplotype clustering, f3/f4 statistics, and qpWave/qpAdm modeling to infer ancestry composition and admixture events.

Results: The Ewenki occupy a genetically distinct position within Northeast Asia and show close genetic affinities with Chinese Mongolic, Tungusic-speaking, and ancient Northeast Asian populations. f3/f4 statistics revealed shared genetic drift and admixture signals linking the Ewenki to ancient Northeast Asian, Siberian, and Yellow River Basin-related populations. qpWave and qpAdm analyses further indicated that the Ewenki can be modeled primarily as a mixture of ancient Northeast Asian/Siberian-related ancestry and ancient Yellow River Basin farmer-related ancestry, reflecting long-term population interactions and admixture in Northeast Asia.

Conclusion: The Ewenki share significant genetic similarities with Tungusic-speaking populations, mainly resulting from admixture between ancient Northeast Asian groups and Yellow River Basin farmers.

Keywords

Evolutionary history / genetic structure / genetic admixture / Ewenki

References

[1] Taliun D,Harris DN,Kessler MD.et al. ; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed program Nature 2021 590 290 9 PMC7875770

[2] All of Us Research Program Genomics Investigators. Genomic data in the all of us research program Nature 2024 627 340 6

[3] He G,Yao H,Duan S.et al. ; 10K_CPGDP Consortium. Pilot work of the 10K Chinese people genomic diversity project along the silk road suggests a complex east-west admixture landscape and biological adaptations Sci China Life Sci 2025 68 914 33

[4] He G,Duan S,Chen G.et al. Human population genetic history and evolutionary dynamics on the Eastern Tibetan plateau Mol Biol Evol 2025 42 msaf258 PMC12620650

[5] He G,Chen J,Duan S.et al. ; 10K_CPGDP Consortium. Largest-scale genomic resource reconstructing the genetic origin, population structure, and biological adaptations of the hui people Mol Biol Evol 2025 42 msaf225 PMC12497895

[6] Lea AJ,Caldas IV,Garske KM.et al. Adaptations to water stress and pastoralism in the Turkana of northwest Kenya Science 2025 389 1246 51

[7] He Y,Zhang X,Peng MS.et al. ; Consortium of Anthropological Research in Southeast Asia and Southwest China (CASEAC). Genome diversity and signatures of natural selection in mainland Southeast Asia Nature 2025 643 417 26

[8] Silcocks M,Farlow A,Hermes A.et al. ; National Centre for Indigenous Genomics. Indigenous Australian genomes show deep structure and rich novel variation Nature 2023 624 593 601 PMC10733150

[9] Reis ALM,Rapadas M,Hammond JM.et al. ; National Centre for Indigenous Genomics. The landscape of genomic structural variation in Indigenous Australians Nature 2023 624 602 10 PMC10733147

[10] Jeong C,Wang K,Wilkin S.et al. A dynamic 6,000-year genetic history of Eurasia’s Eastern steppe Cell 2020 183 890 904.e29 PMC7664836

[11] Gnecchi-Ruscone GA,Szécsényi-Nagy A,Koncz I.et al. Ancient genomes reveal origin and rapid trans-Eurasian migration of 7^th century Avar elites Cell 2022 185 1402 1413.e21 PMC9042794

[12] Lee J,Miller BK,Bayarsaikhan J.et al. Genetic population structure of the Xiongnu Empire at imperial and local scales Sci Adv 2023 9 eadf3904 PMC10104459

[13] Gnecchi-Ruscone GA,Rácz Z,Samu L.et al. Network of large pedigrees reveals social practices of Avar communities Nature 2024 629 376 83 PMC11078744

[14] Wang K,Tobias B,Pany-Kucera D.et al. Ancient DNA reveals reproductive barrier despite shared Avar-period culture Nature 2025 638 1007 14 PMC11864967

[15] Bai H,Guo X,Zhang D.et al. The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations Genome Biol Evol 2014 6 3122 36 PMC4540083

[16] Zerjal T,Xue Y,Bertorelle G.et al. The genetic legacy of the Mongols Am J Hum Genet 2003 72 717 21 PMC1180246

[17] Li Q,Dong K,Xu L.et al. The distribution of three candidate cold-resistant SNPs in six minorities in North China BMC Genomics 2018 19 134 PMC5809914

[18] Lan Q,Zhao C,Wei C,Xu H,Shen C,Zhu B. Genetic insights and evaluation of forensic features in Mongolian and Ewenki groups using the InDel variations Front Biosci 2022 27 67

[19] Wang M,Huang Y,Liu K.et al. ; 10K_CPGDP Consortium. Multiple human population movements and cultural dispersal events shaped the landscape of Chinese paternal heritage Mol Biol Evol 2024 41 PMC11232699

[20] Chang CC,Chow CC,Tellier LC,Vattikuti S,Purcell SM,Lee JJ. Second-generation PLINK: rising to the challenge of larger and richer datasets Gigascience 2015 4 7 PMC4342193

[21] Wang CC,Yeh HY,Popov AN.et al. Genomic insights into the formation of human populations in East Asia Nature 2021 591 413 9

[22] Ning C,Li T,Wang K.et al. Ancient genomes from northern China suggest links between subsistence changes and human migration Nat Commun 2020 11 2700 PMC7264253

[23] Bergström A,McCarthy SA,Hui R.et al. Insights into human genetic variation and population history from 929 diverse genomes Science 2020 367 eaay5012 PMC7115999

[24] Choin J,Mendoza-Revilla J,Arauna LR.et al. Genomic insights into population history and biological adaptation in Oceania Nature 2021 592 583 9

[25] Alexander DH,Novembre J,Lange K. Fast model-based estimation of ancestry in unrelated individuals Genome Res 2009 19 1655 64 PMC2752134

[26] Lawson DJ,Hellenthal G,Myers S,Falush D. Inference of population structure using dense haplotype data PLoS Genet 2012 8 e1002453 PMC3266881

[27] Patterson N,Moorjani P,Luo Y.et al. Ancient admixture in human history Genetics 2012 192 1065 93 PMC3522152

[28] Mallick S,Micco A,Mah M.et al. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes Sci Data 2024 11 182 PMC10858950

[29] Tao L,Yuan H,Zhu K.et al. Ancient genomes reveal millet farming-related demic diffusion from the Yellow River into southwest China Curr Biol 2023 33 4995 5002.e7

[30] Du P,Zhu K,Wang M.et al. Genomic dynamics of the Lower Yellow River Valley since the Early Neolithic Curr Biol 2024 34 3996 4006.e11

[31] Li S,Wang R,Ma H.et al. Ancient genomic time transect unravels the population dynamics of Neolithic middle Yellow River farmers Sci Bull 2024 69 3365 70

[32] Wang F,Wang R,Ma H.et al. Neolithization of Dawenkou culture in the lower Yellow River involved the demic diffusion from the Central Plain Sci Bull 2024 69 3677 81

[33] Xiong J,Wang R,Chen G.et al. Inferring the demographic history of Hexi Corridor over the past two millennia from ancient genomes Sci Bull 2024 69 606 11

[34] Zhu K,Hu C,Yang M.et al. The demic diffusion of Han culture into the Yunnan-Guizhou plateau inferred from ancient genomes Natl Sci Rev 2024 11 nwae387 PMC11647586

[35] Fang H,Liang F,Ma H.et al. Dynamic history of the Central Plain and Haidai region inferred from Late Neolithic to Iron Age ancient human genomes Cell Rep 2025 44 115262

[36] UK Biobank Whole-Genome Sequencing Consortium. Whole-genome sequencing of 490,640 UK Biobank participants Nature 2025 645 692 701

[37] Verma A,Huffman JE,Rodriguez A.et al. Diversity and scale: genetic architecture of 2068 traits in the VA million veteran program Science 2024 385 eadj1182

[38] Yang Q,Sun Y,Duan S.et al. High-quality Population-specific Haplotype-resolved Reference Panel in the Genomic and Pangenomic Eras Genom Proteom Bioinform 2025 23 qzaf022 PMC13175255

[39] Wang Z,Liu K,Yuan H.et al. YanHuang paternal genomic resource suggested a weakly-differentiated multi-source admixture model for the formation of Han’s founding ancestral lineages Genom Proteom Bioinform 2025 23 qzaf049

[40] Wang M,Duan S,Sun Q.et al. Genomic insights into population structure, adaptation, and archaic introgression at the Himalayan-East Asian crossroads J Genet Genomics 2026 53 414 32

[41] Ioannidis AG,Blanco-Portillo J,Sandoval K.et al. Paths and timings of the peopling of Polynesia inferred from genomic networks Nature 2021 597 522 6 PMC9710236

[42] Ioannidis AG,Blanco-Portillo J,Sandoval K.et al. Native American gene flow into Polynesia predating Easter Island settlement Nature 2020 583 572 7 PMC8939867

[43] Malaspinas AS,Westaway MC,Muller C.et al. A genomic history of Aboriginal Australia Nature 2016 538 207 14

[44] Fan S,Spence JP,Feng Y.et al. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation Cell 2023 186 923 939.e14 PMC10568978

[45] Gurdasani D,Carstensen T,Fatumo S.et al. Uganda genome resource enables insights into population history and genomic discovery in Africa Cell 2019 179 984 1002.e36 PMC7202134

[46] Lachance J,Vernot B,Elbers CC.et al. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers Cell 2012 150 457 69 PMC3426505

[47] Skoglund P,Thompson JC,Prendergast ME.et al. Reconstructing prehistoric African population structure Cell 2017 171 59 71.e21 PMC5679310

[48] Joshi E,Biddanda A,Popoola J.et al. ; 54gene Team, NCD-GHS Consortium. Whole-genome sequencing across 449 samples spanning 47 ethnolinguistic groups provides insights into genetic diversity in Nigeria Cell Genom 2023 3 100378

[49] Choudhury A,Aron S,Botigué LR.et al. ; TrypanoGEN Research Group, H3Africa Consortium. High-depth African genomes inform human migration and health Nature 2020 586 741 8

[50] Fortes-Lima CA,Burgarella C,Hammarén R.et al. The genetic legacy of the expansion of Bantu-speaking peoples in Africa Nature 2024 625 540 7 PMC10794141

[51] Gurdasani D,Carstensen T,Tekola-Ayele F.et al. The African Genome Variation Project shapes medical genetics in Africa Nature 2015 517 327 32 PMC4297536

[52] Lipson M,Ribot I,Mallick S.et al. Ancient West African foragers in the context of African population history Nature 2020 577 665 70 PMC8386425

[53] Lipson M,Sawchuk EA,Thompson JC.et al. Ancient DNA and deep population structure in sub-Saharan African foragers Nature 2022 603 290 6 PMC8907066

[54] Hanotte O,Bradley DG,Ochieng JW,Verjee Y,Hill EW,Rege JE. African pastoralism: genetic imprints of origins and migrations Science 2002 296 336 9

[55] Patin E,Lopez M,Grollemund R.et al. Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America Science 2017 356 543 6

[56] Prendergast ME,Lipson M,Sawchuk EA.et al. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa Science 2019 365 eaaw6275 PMC6827346

[57] Zhang P,Luo H,Li Y.et al. ; Han100K Initiative. NyuWa Genome resource: a deep whole-genome sequencing-based variation profile and reference panel for the Chinese population Cell Rep 2021 37 110017

[58] Cao Y,Li L,Xu M.et al. ; ChinaMAP Consortium. The ChinaMAP analytics of deep whole genome sequences in 10,588 individuals Cell Res 2020 30 717 31 PMC7609296

[59] Yang MY,Zhong JD,Li X.et al. SEAD reference panel with 22,134 haplotypes boosts rare variant imputation and genome-wide association analysis in Asian populations Nat Commun 2024 15 10839 PMC11686012

[60] Zhou D,Wu M,Tan Q.et al. Non-coding genetic elements of lung cancer identified using whole genome sequencing in 13,722 Chinese Nat Commun 2025 16 7365 PMC12335547

[61] Jiang T,Guo H,Liu Y.et al. A comprehensive genetic variant reference for the Chinese population Sci Bull 2024 69 3820 5

[62] Lipson M,Cheronet O,Mallick S.et al. Ancient genomes document multiple waves of migration in Southeast Asian prehistory Science 2018 361 92 5 PMC6476732

[63] McColl H,Racimo F,Vinner L.et al. The prehistoric peopling of Southeast Asia Science 2018 361 88 92

[64] Sun Y,Wang M,Sun Q.et al. Distinguished biological adaptation architecture aggravated population differentiation of Tibeto-Burman-speaking people J Genet Genomics 2024 51 517 30

[65] Huang Y,Wang M,Wang Z.et al. Short tandem repeats in populations of the Qinghai-Tibet Plateau and adjacent regions provide insights into high-altitude adaptation Sci Adv 2025 11 eadx1590 PMC12533570

[66] Lin X,Liu Y,Zhang J.et al. Genomic resources from the Yunnan-Guizhou Plateau reveal the linguistic‐linked demographic history and insights into human adaptation and disease of multi‐ancestry populations J Syst Evol 2025 63 1370 89

[67] He G,Sun Y,Duan S.et al. Ancient genomes give insight into 160,000 years of East Asian population dynamics and biological adaptation Genome Biol 2025 26 420

[68] Robbeets M,Bouckaert R,Conte M.et al. Triangulation supports agricultural spread of the Transeurasian languages Nature 2021 599 616 21 PMC8612925

[69] Ma H,Zhou Y,Wang R.et al. Ancient genomes shed light on the long-term genetic stability in the Central Plain of China Sci Bull 2025 70 333 7

[70] Yang T,He J,Li C.et al. Ancient DNA reveals the population interactions and a Neolithic patrilineal community in Northern Yangtze Region Nat Commun 2025 16 8728 PMC12484831

[71] Yang MA,Fan X,Sun B.et al. Ancient DNA indicates human population shifts and admixture in northern and southern China Science 2020 369 282 8

[72] Zhang D,Sun B,Li F.et al. Neolithic genomes reveal long distance interactions in agropastoral border zone of Yan Mountain Region. Sci Bull 2026;71:148-58

[73] Xiong J,Xu Y,Chen G.et al. The genomic history of East Asian Middle Neolithic millet- and rice-agricultural populations Cell Genom 2025 5 100976 PMC12791001

[74] Zou Y,Tan J,Zhou J.et al. Ancient genomes from the Yellow River Bend reveal long-distance population interactions between the Central Plains, Steppe, and southern China Cell Rep 2025 44 116034

[75] Liu J,Liu Y,Zhao Y.et al. East Asian Gene flow bridged by northern coastal populations over past 6000 years Nat Commun 2025 16 1322 PMC11791043

[76] Damgaard PB,Marchi N,Rasmussen S.et al. 137 ancient human genomes from across the Eurasian steppes Nature 2018 557 369 74

[77] Flegontov P,Altınışık NE,Changmai P.et al. Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America Nature 2019 570 236 40 PMC6942545

[78] Sikora M,Pitulko VV,Sousa VC.et al. The population history of northeastern Siberia since the Pleistocene Nature 2019 570 182 8 PMC7617447

[79] Luo L,Wang M,Liu Y.et al. Sequencing and characterizing human mitochondrial genomes in the biobank-based genomic research paradigm Sci China Life Sci 2025 68 1610 25

[80] Moltke I,Grarup N,Jørgensen ME.et al. A common Greenlandic TBC1D4 variant confers muscle insulin resistance and type 2 diabetes Nature 2014 512 190 3

[81] Skoglund P,Mallick S,Bortolini MC.et al. Genetic evidence for two founding populations of the Americas Nature 2015 525 104 8 PMC4982469

[82] Sohail M,Palma-Martínez MJ,Chong AY.et al. Mexican Biobank advances population and medical genomics of diverse ancestries Nature 2023 622 775 83 PMC10600006

[83] Stæger FF,Andersen MK,Li Z.et al. Genetic architecture in Greenland is shaped by demography, structure and selection Nature 2025 639 404 10 PMC11903302

[84] Ziyatdinov A,Torres J,Alegre-Díaz J.et al. ; Regeneron Genetics Center, Mexico City Prospective Study. Genotyping, sequencing and analysis of 140,000 adults from Mexico City Nature 2023 622 784 93

[85] Gusareva ES,Ghosh AG,Kharkov VN.et al. From North Asia to South America: Tracing the longest human migration through genomic sequencing Science 2025 388 eadk5081

[86] Nunes K,Araújo Castro E Silva M,Rodrigues MR.et al. Admixture’s impact on Brazilian population evolution and health Science 2025 388 eadl3564